People sometimes have this idea when they get a 700C or 29er disk brake bike, and realize that there's technically nothing stopping them from using a 26" wheel on there. But apparently it's not without its complications: A bike is made with a given geometry assuming the wheels will be a certain size. If you put 26" wheels on a bike made for 700C then this will lower the bottom bracket, which will probably cause strike issues with the pedals (especially cornering or approaching curbs etc). The handling may also be negatively impacted in ways that are hard to predict. Then there's fenders - they will end up very far away from your 26" tires, if the bike is made for 700C.

When I asked Salsa about putting 700C tires on my 29er Fargo, for example, they advised against using anything much smaller than 50mm, since it would apparently change the ride. So that's not even 26" - just smaller 700C tires! There are obviously issues there. Framebuilding geometry is a very subtle business, small changes can have big impacts. So you can try it, but it's not a slam dunk with no consequences... why don't you talk to the custom builder you're going with, I'm sure they will be able to fill you in on what the potential problems would be. Possibly an ace framebuilder could design a bike that would work from scratch with either wheel size, but I think what you'd end up with is a bike that isn't really optimized for either. Jack of all trades, master of none syndrome. I'd say it's better to just build a 26" expedition tourer, if this is a "round the world" type bike - do it right for that wheel size, and be done with it.

Neil